Expanding LogP: Present possibilities

Functionalization of a Ru(II) polypyridine complex with an aldehyde group as a synthetic precursor for photodynamic therapy

Photodynamic therapy has garnered significant attention over the past decades for its potential in treating various types of cancer, as well as bacterial, fungal, and viral infections. However, current clinically approved photosensitizers based on a tetrapyrrolic scaffold face notable limitations, including low water solubility, slow body clearance, and photobleaching. As a promising alternative, Ru(II) polypyridyl complexes have emerged due to their favorable photophysical and biological properties (i.e., reactive oxygen species generation, high water solubility, and biocompatibility). Despite these attractive properties, the vast majority of compounds are associated with poor tumor accumulation, representing a major hurdle for therapeutic applications. To overcome this limitation, herein, the chemical synthesis and photophysical evaluation of the functionalization of a Ru(II) polypyridyl complex with an aldehyde group, as a synthetic precursor for further conjugation, is reported. To ensure that the intrinsic chemical reactivity of the aldehyde group remains unaffected by the coordination environment to the metal center, a phenyl spacer was strategically introduced between the central ligand framework and the aldehyde functionality. Computational studies indicated that upon excitation of the metal complex, an excited state electron from the ruthenium t2g orbital is transferred to the π* ligand orbital in a metal-to-ligand charge transfer transition. The compound was found to be highly stable under physiological conditions as well as upon irradiation. Upon light exposure, the metal complex was found to efficiently convert molecular oxygen to singlet oxygen. These findings highlight the potential of the aldehyde functionalized Ru(II) polypyridyl complex as a versatile precursor for photodynamic therapy.

Enhancing Blood-Brain Barrier Penetration Prediction by Machine Learning-Based Integration of Novel and Existing, In Silico and Experimental Molecular Parameters from a Standardized Database

Predicting blood-brain barrier (BBB) penetration is crucial for developing central nervous system (CNS) drugs, representing a significant hurdle in successful clinical phase I studies. One of the most valuable properties for this prediction is the polar surface area (PSA). However, molecular structures are missing geometric optimization, which, together with lack of standardization, leads to variations in calculation. Additionally, prediction rules have been established by combining different molecular properties such as the BBB score or CNS multiparameter optimization (CNS MPO). This study aims to create an approach for 3D PSA calculation, to directly apply this value in combination with a set of 23 other parameters in a novel machine learning (ML)-based scoring, and to further evaluate existing prediction models using a standardized database. We developed and analyzed a standardized data set derived from the same laboratory, encompassing 24 calculated and experimentally determined molecular parameters such as PSA from various models, HPLC log P values, and hydrogen bond characteristics for 154 radiolabeled molecules and licensed or well-characterized drugs. These molecules were classified into categories based on BBB penetration, nonpenetration, and interactions with efflux transporters. We supplemented these with a novel in silico 3D calculation of nonclassical PSA. Additionally, we have calculated published prediction rules based on this standardized and transparent database. Using these data, we trained various ML models within a 100-fold Monte Carlo cross-validation framework to derive a novel ML-based prediction score for BBB penetration and validated the three most used existing predictive rules. To interpret the influence of individual molecular parameters and different existing predictive rules, we employed explainable artificial intelligence methods including Shapley additive explanations (SHAP) and surrogate modeling. The ML approach outperformed existing scores for BBB penetration by applying a complex nonlinear integration of molecular properties, with the random forest model achieving the best performance for predicting binary BBB penetration (area under the receiver operating characteristic curve (AUC) 0.88, 95% confidence intervals: 0.87-0.90), and multiclass efflux transporter versus CNS-positive and CNS-negative prediction (AUC 0.82, 95% CI: 0.81-0.82). SHAP analysis revealed the multifactorial nature of the problem, highlighting the advantage of multivariate models over single predictive parameters. The ML model's superior predictive capability was demonstrated in comparison with existing scoring systems, like the CNS MPO (AUC 0.53), the CNS MPO Positron emission tomography (PET) (AUC 0.51), and BBB score (AUC 0.68) while also enabling the identification of efflux transporter substrates and inhibitors. Our integrated ML approach, combining experimental and in silico measurements with novel in silico methods based on a standardized database including a plethora of different substance groups (licensed drugs and in vivo evaluated PET tracers), enhances the prediction of BBB penetration. This approach may reduce the reliance on extensive experimental measurements and animal testing, accelerating CNS drug development.

6-aryloxy-2-aminopyrimidine-benzonitrile hybrids as anti-infective agents: Synthesis, bioevaluation, and molecular docking

This report explores the potential of novel 6-aryloxy-2-aminopyrimidine-benzonitrile scaffolds as promising anti-infective agents in the face of the increasing threat of infectious diseases. Starting from 2-amino-4,6-dichloropyrimidine, a series of 24 compounds inspired from the antiviral drugs dapivirine, etravirine, and rilpivirine were designed and synthesized via a two-step reaction sequence in good yields. Biological testing of synthetic analogs revealed potent inhibition against both viral and tuberculosis targets. Notably, compounds 5p (2,4-dimethyl substitution; IC50 = 44 ± 4.9 µM; selectivity index [SI] = 20) and 5 s (3-thiophenphenyl; IC50 = 6 ± 1 µM; SI = 120) showed significant antiviral activity against pandemic influenza virus A/Puerto Rico/8/34 (H1N1) with positive toxicity profiles and also exhibited good IC50 values (5p, IC50 = 10 ± 2 µM; SI = 9 and 5 s, IC50 = 16 ± 2 µM; SI = 60) against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Wuhan strain) compared with favipiravir. In addition, analogs 5a, 5r, 5t, and 5u showed good antitubercular activity against Mycobacterium tuberculosis H37Rv strain and compounds 3, 5f, 5n, and 5q showed moderate antibacterial activity against gram+ve and gram-ve bacterial strains, suggesting that this scaffold has a broad spectrum of therapeutic effects.

Dihydrobenzothiazole coupled N-piperazinyl acetamides as antimicrobial agents: Design, synthesis, biological evaluation and molecular docking studies

Substituted saturated N-heterocycles have gained momentum as effective scaffolds for the development of new drugs. In this study, we coupled partly saturated benzothiazoles with substituted piperazines and evaluated their antimicrobial activity. Following a three-step reaction sequence from commercially available cyclic 1,3-diones, a series of novel 2-[4-substituted-1-piperazinyl]-N-(7-oxo-4,5,6,7-tetrahydrobenzo[d]thiazol-2-yl)acetamides (7a-af) were synthesised. 2-Amino-5,6-dihydro-benzo[d]thiazol-7(4H)-ones, obtained through the condensation of cyclohexane-1,3-diones with thiourea, were acetylated with chloroacetic chloride and then reacted with N-substituted piperazines 6a-p to give the desired products 7a-af in excellent yields. All 32 new compounds were fully characterised by their 1 H-nuclear magnetic resonance (NMR), 13 C-NMR and high-resolution mass spectrometry spectra. The synthetic compounds 7a-af were tested in vitro for their efficacy as antimicrobials against pathogenic strains of Gram-positive and Gram-negative bacteria, Streptococcus mutans and Salmonella typhi, respectively, as well as against fungal strains, including Candida albicans 3018 and C. albicans 4748. Ciprofloxacin and fluconazole served as the reference drugs. While compounds 7c and 7l showed inhibition against fungal strains with zones of inhibition of 11 and 1 mm, respectively, four analogues (7d, 7l, 7n, and 7r) demonstrated strong antibacterial action (zone of inhibition in the range of 10-15 mm). Three compounds (7j, 7l, and 7w) also exhibited moderate antitubercular activity (MIC: 6.25 µg/mL) against Mycobacterium tuberculosis H37Rv. Molecular docking investigations and the predicted physicochemical and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties for the potent compounds made this scaffold useful as a pharmacologically active framework for the development of potential antimicrobial hits.

N-Substituted piperazine-coupled imidazo[2,1-b]thiazoles as inhibitors of Mycobacterium tuberculosis: Synthesis, evaluation, and docking studies

An innovative series of N-substituted piperazine-linked imidazothiazole derivatives 7(a-x) were synthesized, and their antitubercular effectiveness was evaluated. A three-step reaction sequence involving the condensation of 1,3-dichloroacetone and thiourea, coupling with substituted piperazines to give the intermediates 5(a-d) and cyclization with substituted α-bromoacetophenones produced the desired imidazothiazole derivatives 7(a-x) in excellent yields. In vitro screening of new derivatives against Mycobacterium tuberculosis H37Rv resulted in 7k (minimum inhibitory concentration [MIC]: 0.78 μg/mL) and 7g and 7h (MIC: 1.56 μg/mL) as potent hit compounds. Further, the docking studies of the promising compounds 7k, 7g, and 7h revealed that the best molecular interactions are with the DprE1 in complex with sulfonyl PBTZ of M. tuberculosis as the target protein (PDB ID: 6G83).

Synthesis and biological evaluation of novel 18F-labeled 2,4-diaminopyrimidine derivatives for detection of ghrelin receptor in the brain

The ghrelin receptor (GHSR) is known to regulate various physiological processes including appetite, food intake, and growth hormone release. Its expression is mainly observed in the brain, pancreas, stomach, and intestine. However, the functions of the receptor have not been fully elucidated. GHSR imaging with positron emission tomography (PET) is expected to further understanding of the functions and pathologies of the receptor. In this study, we newly designed and synthesized diaminopyrimidine derivatives ([18F]BPP-1 and [18F]BPP-2) and evaluated their utility as novel PET probes targeting GHSR. In in vitro competitive binding assays, the binding affinity of BPP-2 for GHSR (Ki = 274 nM) was comparable to that of the diaminopyimidine lead compound Abb8a (Ki = 109 nM). In a biodistribution study using normal mice, [18F]BPP-2 displayed low uptake in the brain and moderate uptake in the pancreas, but high radioactivity accumulation in bone was observed due to its defluorination in vivo. Taken together, although further improvement of the pharmacokinetics is needed, the diaminopyrimidine scaffold has potential for the development of useful GHSR-targeting PET probes.

Complexity of αvβ6-integrin targeting RGD peptide trimers: emergence of non-specific binding by synergistic interaction

Multimerization is an established strategy to design bioactive macromolecules with enhanced avidity, which has been widely employed to increase the target-specific binding and uptake of imaging probes and pharmaceuticals. However, the factors governing the general biodistribution of multimeric probes are less well understood but are nonetheless decisive for their clinical application. We found that regiospecific exchange of phenylalanine by tyrosine (chemically equivalent to addition of single oxygen atoms) can have an unexpected, dramatic impact on the in vivo behavior of gallium-68 labeled αvβ6-integrin binding peptides trimers. For example, introduction of one and two Tyr, equivalent to just 1 and 2 additional oxygens and molecular weight increases of 0.38% and 0.76% for our >4 kDa constructs, reduced non-specific liver uptake by 50% and 72%, respectively. The observed effect did not correlate to established polarity measures such as log D, and generally defies explanation by reductionist approaches. We conclude that multimers should be viewed not just as molecular combinations of peptides whose properties simply add up, but as whole entities with higher intrinsic complexity and thus a strong tendency to exhibit newly emerged properties that, on principle, cannot be predicted from the characteristics of the monomers used.

Synthesis, characterization and anti-breast cancer activities of stachydrine derivatives

Stachydrine is a hydrophilic quaternary amine salt with good antitumor effect, but its application is limited due to its rapid metabolism and low bioavailability. We synthesized and evaluated nine prodrugs of stachydrine, which showed suitable hydrophobicity (CLogP: -2.58-4.78, vs SS-0: -3.32) and better in vitro anticancer activity (IC50: 0.34 μM-14.03 mM, vs SS-0: 38.97 mM-147.19 mM) in comparison with stachydrine. Among them, SS-12, SS-16 and SS-18 are the most effective compounds against 4T1 cells, and the IC50 is 2.15-24.14 μM. Especially, compared with stachydrine, SS-12 significantly blocked the cell cycle in the G0/G1 phase, reduced the mitochondrial membrane potential, and induced the apoptosis of 4T1 cells through mitochondria pathway, which increased the expressions of Bax and cleaved caspase-3 protein, decrease the expression of Bcl-2. The pharmacokinetics of SS-12 showed a rational bioavailability (79.6%), and a longer retention time (T1/2 = 7.62 h) than that of stachydrine (T1/2 ≈ 1.16 h) in rats. Compared with stachydrine, SS-12 significantly enhanced the anticancer efficacy (56.32% of tumor-inhibition rates, vs SS-0: 3.89%), meanwhile, ameliorated the tumor-induced organ damage in mice. Therefore, SS-12 may be a promising prodrug of stachydrine against breast cancer.

Bioinformatics Tools for the Analysis of Active Compounds Identified in Ranunculaceae Species

The chemical compounds from extracts of three Ranunculaceae species, Aconitum toxicum Rchb., Anemone nemorosa L. and Helleborus odorus Waldst. & Kit. ex Willd., respectively, were isolated using the HPLC purification technique and analyzed from a bioinformatics point of view. The classes of compounds identified based on the proportion in the rhizomes/leaves/flowers used for microwave-assisted extraction and ultrasound-assisted extraction were alkaloids and phenols. Here, the quantifying of pharmacokinetics, pharmacogenomics and pharmacodynamics helps us to identify the actual biologically active compounds. Our results showed that (i) pharmacokinetically, the compounds show good absorption at the intestinal level and high permeability at the level of the central nervous system for alkaloids; (ii) regarding pharmacogenomics, alkaloids can influence tumor sensitivity and the effectiveness of some treatments; (iii) and pharmacodynamically, the compounds of these Ranunculaceae species bind to carbonic anhydrase and aldose reductase. The results obtained showed a high affinity of the compounds in the binding solution at the level of carbonic anhydrases. Carbonic anhydrase inhibitors extracted from natural sources can represent the path to new drugs useful both in the treatment of glaucoma, but also of some renal, neurological and even neoplastic diseases. The identification of natural compounds with the role of inhibitors can have a role in different types of pathologies, both associated with studied and known receptors such as carbonic anhydrase and aldose reductase, as well as new pathologies not yet addressed.

Pyrazole-based lamellarin O analogues: synthesis, biological evaluation and structure-activity relationships

A library of pyrazole-based lamellarin O analogues was synthesized from easily accessible 3(5)-aryl-1H-pyrazole-5(3)-carboxylates which were subsequently modified by bromination, N-alkylation and Pd-catalysed Suzuki cross-coupling reactions. Synthesized ethyl and methyl 3,4-diaryl-1-(2-aryl-2-oxoethyl)-1H-pyrazole-5-carboxylates were evaluated for their physicochemical property profiles and in vitro cytotoxicity against three human colorectal cancer cell lines HCT116, HT29, and SW480. The most active compounds inhibited cell proliferation in a low micromolar range. Selected ethyl 3,4-diaryl-1-(2-aryl-2-oxoethyl)-1H-pyrazole-5-carboxylates were further investigated for their mode of action. Results of combined viability staining via Calcein AM/Hoechst/PI and fluorescence-activated cell sorting data indicated that cell death was triggered in a non-necrotic manner mediated by mainly G2/M-phase arrest.

Synthesis, biological evaluation and molecular docking study of some new 4-aminosalicylic acid derivatives as anti-inflammatory and antimycobacterial agents

In this study, new derivatives of the antitubercular and anti-inflammatory drug, 4-aminosaliclic acids (4-ASA) were synthesized, characterized, and evaluated for these activities. In vivo and in viro evaluation of anti-inflammatory activity revealed that compounds 10, 19 and 20 are the most active with potent cyclooxygenase-2 (COX-2) and 5-lipooxgenase (5-LOX) inhibition and without causing gasric lesions. The minimum inhibitory concentrations (MIC) of the newly synthesized compound were, also, measured against Mycobacterium tuberculosis H37RV. Among the tested compounds 17, 19 and 20 exhibited significant activities against the growth of M. tuberculosis. 20 is the most potent with (MIC 1.04 µM) 2.5 folds more potent than the parent drug 4-ASA. 20 displayed low cytotoxicity against normal cell providing a high therapeutic index. Important structure features were analyzed by docking and structure-activity relationship analysis to give better insights into the structural determinants for predicting the anti-inflammatory and anti-TB activities. Our results indicated that compounds 19 and 20 are potential lead compounds for the discovery of dual anti-inflammatory and anti-TB drug candidates.

Prediction of the endocrine-disrupting ability of 49 per- and polyfluoroalkyl substances: In silico and epidemiological evidence

The toxic effects of per- and polyfluoroalkyl substances (PFASs) on humans are mediated by nuclear hormone receptors (NHRs). However, data on the interaction of PFASs and NHRs is limited. Endocrine Disruptome, an inverse docking tool, was used in this study to simulate the docking of 49 common PFASs with 14 different types of human NHRs. According to the findings, 25 PFASs have a high or moderately high probability of binding to more than five NHRs, with androgen receptor (AR) and mineralocorticoid receptor (MR) being the most likely target NHRs. Molecular docking analyses revealed that the binding modes of PFASs with the two NHRs were similar to those of their corresponding co-crystallized ligands. PFASs, in particular, may disrupt the endocrine system by binding to MR. This finding is consistent with epidemiological research that has linked PFASs to MR-related diseases. Our findings may contribute to a better understanding of the health risks posed by PFASs.

Synthesis of Paeonol-Ozagrel Conjugate: Structure Characterization and In Vivo Anti-Ischemic Stroke potential

Ischemic stroke is a common neurological disease that can lead to mortality and disability. The current curative effect remains unsatisfactory because drug accumulation in the diseased areas is insufficient as a result of the unique blood–brain barrier. Therefore, much attention has been paid to develop a novel therapeutic compound, paeonol-ozagrel conjugate (POC), for ischemic stroke. Then, POC was successfully synthesized by conjugating of paeonol and ozagrel as mutual prodrug. A series of in vitro characterizations and evaluations, including high - resolution mass spectroscopy, nuclear magnetic resonance spectroscopy, partition coefficient, and assessment of cytotoxicity against PC12 cells, were performed. Pharmacokinetic study demonstrated POC is eliminated quickly (t_1/2 = 53.46 ± 19.64 min), which supported a short dosing interval. The neurological score, infarct volume, histopathological changes, oxidative stress, inflammatory cytokines levels, and TXA₂ levels also were evaluated in vivo in middle cerebral artery occlusion (MCAO) rats. All results showed that POC had a significant curative and therapeutic effect on ischemic stroke, as evaluated by the middle cerebral artery occlusion. Overall, POC can be expected to become a new drug candidate for the treatment of ischemic stroke.

Antileishmanial activity of synthetic analogs of the naturally occurring quinolone alkaloid N-methyl-8-methoxyflindersin

Leishmaniasis is a neglected, parasitic tropical disease caused by an intracellular protozoan from the genus Leishmania. Quinoline alkaloids, secondary metabolites found in plants from the Rutaceae family, have antiparasitic activity against Leishmania sp. N-methyl-8-methoxyflindersin (1), isolated from the leaves of Raputia heptaphylla and also known as 7-methoxy-2,2-dimethyl-2H,5H,6H-pyran[3,2-c]quinolin-5-one, shows antiparasitic activity against Leishmania promastigotes and amastigotes. This study used in silico tools to identify synthetic quinoline alkaloids having structure similar to that of compound 1 and then tested these quinoline alkaloids for their in vitro antiparasitic activity against Leishmania (Viannia) panamensis, in vivo therapeutic response in hamsters suffering from experimental cutaneous leishmaniasis (CL), and ex vivo immunomodulatory potential in healthy donors' human peripheral blood (monocyte)-derived macrophages (hMDMs). Compounds 1 (natural), 2 (synthetic), and 8 (synthetic) were effective against intracellular promastigotes (9.9, 3.4, and 1.6 μg/mL medial effective concentration [EC50], respectively) and amastigotes (5.07, 7.94, and 1.91 μg/mL EC50, respectively). Compound 1 increased nitric oxide production in infected hMDMs and triggered necrosis-related ultrastructural alterations in intracellular amastigotes, while compound 2 stimulated oxidative breakdown in hMDMs and caused ultrastructural alterations in the parasite 4 h posttreatment, and compound 8 failed to induce macrophage modulation but selectively induced apoptosis of infected hMDMs and alterations in the intracellular parasite ultrastructure. In addition, synthetic compounds 2 and 8 improved the health of hamsters suffering from experimental CL, without evidence of treatment-associated adverse toxic effects. Therefore, synthetic compounds 2 and 8 are potential therapeutic candidates for topical treatment of CL.

Enhanced arecoline derivatives as muscarinic acetylcholine receptor M1 ligands for potential application as PET radiotracers

Supported by their involvement in many neurodegenerative disorders, muscarinic acetylcholine receptors (mAChRs) are an interesting target for PET imaging. Nevertheless, no radiotracer is established in clinical routine. Within this work we aim to develop novel PET tracers based on the structure of arecoline. Fifteen novel arecoline derivatives were synthesized, characterized and tested for their affinity to the mAChRs M1-M5 and the conceivable off-target acetylcholinesterase. Five arecoline derivatives and arecoline were labeled with carbon-11 in good yields. Arecaidine diphenylmethyl ester (3b), arecaidine bis(4-fluorophenyl)methyl ester (3c) and arecaidine (4-bromophenyl)(4-fluorophenyl)methyl ester (3e) showed a tremendous gain in mAChR affinity compared to arecoline and a pronounced subtype selectivity for M1. Metabolic stability and serum protein binding of [¹¹C]3b and [¹¹C]3c were in line with properties of established brain tracers. Nonspecific binding of [¹¹C]3c was prevalent in kinetic and endpoint experiment on living cells as well as in autoradiography on native mouse brain sections, which motivates us to decrease the lipophilicity of this substance class prior to in vivo experiments.

Synthesis of novel morpholine, thiomorpholine and N-substituted piperazine coupled 2-(thiophen-2-yl)dihydroquinolines as potent inhibitors of Mycobacterium tuberculosis

A series of novel morpholine, thiomorpholine and N-substituted piperazine coupled 2-(thiophen-2-yl)dihydroquinolines 7a-p was designed and synthesized from 2-acetyl thiophene in six step reaction sequence involving modified Bohlmann-Rahtz and Vilsmeier-Haack-Arnold reactions as key transformations. 2-(Thiophen-2-yl)dihydroquinoline was formylated and subsequently chlorinated using DMF-POCl₃. The resulting aldehyde was reduced to give an alcohol and then converted to bromide using PBr_3. Further coupling of bromide with morpholine, thiomorpholine and N-substituted piperazines resulted in the desired quinolines 7a-p in very good yields. All the new derivatives 7a-p were characterized by their NMR and mass spectral analysis. In vitro screening of new compounds for antimycobacterial activity against Mycobacterium tuberculosis H37Rv (MTB), resulted in two derivatives 7f and 7p as most potent antitubercular agents (MIC:1.56 μg/mL) with lower cytotoxicity profiles.

Polymorphic and Quantum Chemistry Characterization of Candesartan Cilexetil: Importance for the Correct Drug Classification According to Biopharmaceutics Classification System

The recommended method for the biopharmaceutical evaluation of drug solubility is the shake flask; however, there are discrepancies reported about the solubility of certain compounds measured with this method, one of them is candesartan cilexetil. The present work aimed to elucidate the solubility of candesartan cilexetil by associating others assays such as stability determination, polymorphic characterization and in silico calculations of intrinsic solubility, ionized species, and electronic structures using quantum chemistry descriptors (frontier molecular orbitals and Fukui functions). For the complete biopharmaceutical classification, we also reviewed the permeability data available. The polymorphic form used was previously identified as the form I of candesartan cilexetil. The solubility was evaluated in biorelevant media in the pH range of 1.2-6.8 at 37.0°C according to the stability previously assessed. The solubility of candesartan cilexetil is pH dependent and the dose/solubility ratios obtained demonstrated the low solubility of the prodrug. The in silico calculations supported the found results and evidenced the main groups involved in the solvation, benzimidazole, and tetrazol-biphenyl. The human absolute bioavailability reported demonstrates that candesartan cilexetil has low permeability and when associated with the low solubility allows to classify it as class 4 of the Biopharmaceutics Classification System.